Does the time of Fajr (dawn) prayer start after the first Athaan (call for prayer), or the second one?
All perfect praise be to Allah,The Lord of The Worlds The time of Fajr prayer starts after the second Adhan. And Allah Knows Best.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
What is the ruling on water present on the floor of a toilet/bathroom?
The default ruling is the purity of this water present on the bathroom floor. If one is certain or strongly suspects its impurity, then one washes whatever part of the body or clothing this impure water has touched. If one doubts its impurity, the default is purity, and we do not rule it impure based on mere doubt. And Allah the Almighty knows best.
What is the ruling on the ablution of one who touches women prohibited to him by a temporary prohibition (mahram bi-hurma mu'aqqata)?
It is prohibited to touch a woman who is temporarily prohibited (meaning one whom it becomes permissible to marry after the impediment is removed, such as the wife of a brother or paternal uncle). Touching her without a barrier invalidates ablution. And Allah the Almighty knows best.